Wow! I didn't know about metatheme before, but it's really cool (and I believe I've used it without knowing, always when I use qt or java apps).
In some way Windows applications are just a different toolkit. Even when Wine will be more advanced, more stable and better integrated, it will only be as good as another "foreign" toolkit. Thus besides the efforts of high priority (the big things like audio, dib-engine etc.) I think it is worth to blend Wine apps also visually as good as possible into the system.
Tell me if you find out more or if there is something I could help (but I don't know much programming).